High affinity nerve growth factor receptor
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 381–698 | Not recorded | FQD 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one × 1 GOL GLYCEROL × 1 FQM 5-{[5-(6-aminopyridin-2-yl)-2-chlorobenzene-1-carbonyl]amino}-1-phenyl-1H-pyrazole-3-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.63；294 K；Well volume: 30.0 uL Well Ingredients: Salt: 0.2571428571 M (1.9285714282 uL of stock 4.0 M) potassium formate Precipitant: 20.0 %w/v (12.0 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (3.0 uL of stock 1.0 M) Tris (pH 7.63) Plate setup temperature: 13 C Plate incubation temperature: 21 C Drop volume from well: 0.1 uL Drop protein volume: 0.3 uL Protein: 6.00 mg/mL (0.17 mM) Compound1: small molecule to aid crystallization (1.20 mM) Soak of 10mM compound 3 for > 1h into co-crystals of TrkA + compound1 | Resolution 1.87 Å R-free 0.210 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 6D1Z | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1HE7 Human Nerve growth factor receptor TrkA Deposited 2000-11-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
282–413（132 aa）
Fragment：LIGAND BINDING DOMAIN, SPANS RESIDUES 285-380
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.7；10 MG/ML PROTEIN + 0.1-0.3M NACL, 0.1M NA-CITRATE, PH 4.6 - 4.8
|
Resolution 2.00 Å R-free 0.276 |
| 1SHC SHC PTB DOMAIN COMPLEXED WITH A TRKA RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
489–500（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain X
278–408（131 aa）
Fragment：LIGAND BINDING DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.50 Å R-free 0.258 |
| 1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain Y
278–408（131 aa）
Fragment：LIGAND BINDING DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.50 Å R-free 0.258 |
| 1WWA NGF BINDING DOMAIN OF HUMAN TRKA RECEPTOR Deposited 1999-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain X
278–408（131 aa）
Fragment：LIGAND BINDING DOMAIN
Chain Y
278–408（131 aa）
Fragment：LIGAND BINDING DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.50 Å R-free 0.258 |
| 1WWW NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR Deposited 1999-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain X
282–382（101 aa）
Fragment：DOMAIN 5
Chain Y
282–382（101 aa）
Fragment：DOMAIN 5
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5；pH 5.0
|
Resolution 2.20 Å R-free 0.266 |
| 2IFG Structure of the extracellular segment of human TRKA in complex with nerve growth factor Deposited 2006-09-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
36–382（347 aa）
Chain B
36–382（347 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；PEG, GLYCINE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.50
|
Resolution 3.40 Å R-free 0.331 |
| 2N90 TrkA transmembrane domain NMR structure in DPC micelles Deposited 2015-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
410–447（38 aa）
Chain B
410–447（38 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.9；318 K；Pressure ambient
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] protein, 1 mM protein, 40 mM [U-100% 2H] DPC, 20 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 4AOJ Human TrkA in complex with the inhibitor AZ-23 Deposited 2012-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric |
Chain A
473–796（324 aa）
Fragment：KINASE DOMAIN, RESIDUES 473-796
Chain B
473–796（324 aa）
Fragment：KINASE DOMAIN, RESIDUES 473-796
Chain C
473–796（324 aa）
Fragment：KINASE DOMAIN, RESIDUES 473-796
|
Not recorded | V4Z 5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine × 12 ZN ZINC ION × 24 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING DROP METHOD. 1 UL TRKA AT 10 MG/ML IN 10 MG/ML IN 20 MM TRIS PH 8.5, 0.1% CHAPS, 1MM TCEP, 8.7% GLYCEROL MIXED WITH 1 UL MOTHER LIQUOR CONTAINING 35% W/V GLYCEROL, 140 MM NA/K TARTRATE, 100 MM HEPES PH 8.0 SUPPLEMENTED WITH 40 MM ZINC CHLORIDE.
|
Resolution 2.75 Å R-free 0.242 |
| 4CRP Solution structure of a TrkAIg2 domain construct for use in drug discovery Deposited 2014-02-28 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
282–383（102 aa）
Fragment：EXTRACELLULAR NGF BINDING DOMAIN, RESIDUES 270-383
|
Mutation：YES | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.9；293 K；Ionic strength (raw mmCIF value) 10；Pressure 1.0
NMR sample composition
90% H2O, 10% D2O
|
Resolution not provided |
| 4F0I Crystal structure of apo TrkA Deposited 2012-05-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
Fragment：UNP residues 498-796
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1 M Na citrate, pH 5.6, 14% PEG 3350, 5% 2-Propanol , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.241 |
| 4F0I Crystal structure of apo TrkA Deposited 2012-05-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
498–796（299 aa）
Fragment：UNP residues 498-796
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1 M Na citrate, pH 5.6, 14% PEG 3350, 5% 2-Propanol , VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.241 |
| 4GT5 Crystal structure of the inactive TrkA kinase domain Deposited 2012-08-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
Fragment：receptor tyrosine kinase (UNP residues 498-796)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；294.15 K；1.5 M sodium chloride, 0.1 M MES, pH 6.5, 0.2 M sodium/potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
|
Resolution 2.40 Å R-free 0.248 |
| 4PMM The structure of TrkA kinase bound to the inhibitor N-(3-cyclopropyl-1-phenyl-1H-pyrazol-5-yl)-2-{4-[3-methoxy-4-(4-methyl-1H-imidazol-1-yl)phenyl]-1H-1,2,3-triazol-1-yl}acetamide Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
501–787（287 aa）
Fragment：kinase domain (UNP residues 501-787)
|
Not recorded | 31V N-(3-cyclopropyl-1-phenyl-1H-pyrazol-5-yl)-2-{4-[3-methoxy-4-(4-methyl-1H-imidazol-1-yl)phenyl]-1H-1,2,3-triazol-1-yl}acetamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate
|
Resolution 2.00 Å R-free 0.199 |
| 4PMP The structure of TrkA kinase bound to the inhibitor 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
501–787（287 aa）
Fragment：kinase domain (UNP residues 501-787)
|
Not recorded | 31W 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate
|
Resolution 1.80 Å R-free 0.185 |
| 4PMS The structure of TrkA kinase bound to the inhibitor 4-naphthalen-1-yl-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
501–787（287 aa）
Fragment：kinase domain (UNP residues 501-787)
|
Not recorded | 31X 4-(naphthalen-1-yl)-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate
|
Resolution 2.80 Å R-free 0.240 |
| 4PMT The structure of TrkA kinase bound to the inhibitor N~4~-(4-morpholin-4-ylphenyl)-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
501–787（287 aa）
Fragment：kinase domain (UNP residues 501-787)
|
Not recorded | 31Y N~4~-[4-(morpholin-4-yl)phenyl]-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris, 2.3M AmmoniumAcetate
|
Resolution 2.10 Å R-free 0.209 |
| 4YNE (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors Deposited 2015-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
502–796（295 aa）
|
Not recorded | 4EK 6-[(2R)-2-(3-fluorophenyl)pyrrolidin-1-yl]-3-(pyridin-2-yl)imidazo[1,2-b]pyridazine × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0
|
Resolution 2.02 Å R-free 0.216 |
| 4YPS (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors Deposited 2015-03-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
502–796（295 aa）
|
Not recorded | 4F6 4-{6-[(3R)-3-(3-fluorophenyl)morpholin-4-yl]imidazo[1,2-b]pyridazin-3-yl}benzonitrile × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.8M (NH4)2SO4, 0.1M Citrate pH 5.0
|
Resolution 2.10 Å R-free 0.257 |
| 5H3Q Crystal Structure of TrkA kinase with ligand Deposited 2016-10-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
473–796（324 aa）
|
Not recorded | 7HF 1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1.2M Sodium Tartrate, 100mM Tris-HCl pH 8.5, 5 mM DTT
|
Resolution 2.10 Å R-free 0.215 |
| 5I8A TrkA with (6~{R})-3-methylsulfanyl-6-phenyl-1-(1~{H}-pyrazol-3-yl)-6,7-dihydro-5~{H}-thieno[3,4-c]pyridin-4-one Deposited 2016-02-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
400–689（290 aa）
Fragment：catalytic domain, UNP residues 400-689
|
Not recorded | 69C (6R)-3-(methylsulfanyl)-6-phenyl-1-(1H-pyrazol-3-yl)-6,7-dihydrothieno[3,4-c]pyridin-4(5H)-one × 1 CL CHLORIDE ION × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris pH 6.5, 2.3M Ammonium Acetate
|
Resolution 2.33 Å R-free 0.209 |
| 5JFS Crystal structure of TrkA in complex with PF-00593174 Deposited 2016-04-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
404–698（295 aa）
|
Not recorded | 6K0 N-{4-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-2-yl}-N'-(2,4-difluorophenyl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
|
Resolution 2.07 Å R-free 0.191 |
| 5JFV Crystal structure of TrkA in complex with PF-05206283 Deposited 2016-04-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
404–698（295 aa）
|
Not recorded | 6K1 N-{5-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(4-chlorophenyl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
|
Resolution 1.59 Å R-free 0.192 |
| 5JFW Crystal structure of TrkA in complex with PF-05247452 Deposited 2016-04-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
404–698（295 aa）
|
Not recorded | 6K2 2-(4-cyanophenyl)-N-{5-[7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
|
Resolution 1.52 Å R-free 0.209 |
| 5JFX Crystal structure of TrkA in complex with PF-06273340 Deposited 2016-04-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
404–698（295 aa）
|
Not recorded | 6K4 N-{5-[2-amino-7-(1-hydroxy-2-methylpropan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}-2-(5-chloropyridin-2-yl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
|
Resolution 1.63 Å R-free 0.232 |
| 5KMI TrkA JM-kinase with 1-(9{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea Deposited 2016-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Not recorded | 6UE 1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 1.87 Å R-free 0.247 |
| 5KMJ TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1-yl]acetamide Deposited 2016-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Not recorded | 6UF ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.04 Å R-free 0.226 |
| 5KMK TrkA JM-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3-pyridyl]-4-(trifluoromethyl)benzamide Deposited 2016-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Not recorded | 6UG 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.24 Å R-free 0.281 |
| 5KML TrkA JM-kinase with 1-(5-methyl-3-phenyl-1,2-oxazol-4-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea Deposited 2016-06-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6UH 1-(5-methyl-3-phenyl-1,2-oxazol-4-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.01 Å R-free 0.232 |
| 5KMM TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1-naphthyl)urea Deposited 2016-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Not recorded | 6UJ 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.12 Å R-free 0.264 |
| 5KMN TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea Deposited 2016-06-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP residues 376-698
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 6UK 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.14 Å R-free 0.222 |
| 5KMO TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyridyl)urea Deposited 2016-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
376–698（323 aa）
Fragment：catalytic domain with juxtamembrane region, UNP resdiues 376-698
|
Not recorded | 6UM 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
|
Resolution 2.67 Å R-free 0.243 |
| 5KVT THE STRUCTURE OF TRKA KINASE DOMAIN BOUND TO THE INHIBITOR ENTRECTINIB Deposited 2016-07-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
501–787（287 aa）
Fragment：kinase domain (UNP residues 501-787)
|
Not recorded | YMX Entrectinib × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；277 K；VAPOR DIFFUSION, HANGING DROP,
WELL SOLUTION: 0.1M BIS-TRIS, PH6.5, 2.6-3.0M AMMONIUMACETATE
TEMPERATURE 277K
|
Resolution 2.45 Å R-free 0.239 |
| 5WR7 Crystal structure of Trk-A complexed with a selective inhibitor CH7057288 Deposited 2016-11-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
489–792（304 aa）
Fragment：KINASE DOMAIN, UNP residues 489-792
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | RCH N-tert-butyl-2-[2-[6,6-dimethyl-8-(methylsulfonylamino)-11-oxidanylidene-naphtho[2,3-b][1]benzofuran-3-yl]ethynyl]-6-methyl-pyridine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；0.05-0.15M KH2PO4, 0.1M MES pH 6.25, 1.5-2.5M NaCl, 0.05-0.15M NaH2PO4, 0.01M TCEP HCl
|
Resolution 2.76 Å R-free 0.234 |
| 6D1Y Crystal structure of Tyrosine-protein kinase receptor in complex with 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide Inhibitor Deposited 2018-04-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Not recorded | FQJ 2,4-dichloro-N-(3-methyl-1-phenyl-1H-pyrazol-5-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Well volume: 25.0 uL
Well Ingredients:
Buffer: 0.1 M (5.0 uL of stock 0.5 M) ADA (pH 6.50)
Salt: 3.0 M (9.375 uL of stock 8.0 M) lithium nitrate
Plate setup temperature: 13 C
Plate incubation temperature: 4 C
Drop volume from well: 0.1 uL
Drop protein volume: 0.1 uL
Protein Formulation Composition:
Protein: (5.0 mg/mL) (0.14 mM)
Compound: (3.00 mM)
|
Resolution 1.93 Å R-free 0.224 |
| 6D20 Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one and 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide Inhibitors Deposited 2018-04-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Not recorded | FQD 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one × 1 FQG 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；Well volume: 30.0 uL
Well Ingredients:
Polymer: 10.0 %w/v (6.0 uL of stock 50.0 %w/v) PEG 3350
Buffer: 16.0 %v/v (4.8 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Organic (non-volatile): 10.0 %v/v (3.0 uL of stock 100.0 %v/v) Ethylene glycol
Additive: 0.025 M (1.5 uL of stock 0.5 M) TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
Drop volume from well: 0.2 uL
Drop protein volume: 0.4 uL
Protein: 6.30 mg/mL (0.17 mM)
Compound1: 1.00 mM (to aid crystallization).
Compound23 (allostric inhibitor): 1.3ul 50mM compound23 DMSO stock in 133ul protein (0.50 mM)
|
Resolution 1.94 Å R-free 0.207 |
| 6DKB Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10b. Deposited 2018-05-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Not recorded | FKY 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-5-(1-methyl-1H-imidazol-4-yl)pyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Well volume: 30.0 uL
Drop volume from well: 0.2 uL
Drop protein volume: 0.4 uL
Well Ingredients:
Polymer: 10.0 %w/v (6.0 uL of stock 50.0 %w/v) PEG 3350
Buffer: 16.0 %v/v (4.8 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Organic (non-volatile): 10.0 %v/v (3.0 uL of stock 100.0 %v/v) Ethylene glycol
Additive: 0.025 M (1.5 uL of stock 0.5 M) TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
|
Resolution 2.68 Å R-free 0.245 |
| 6DKG Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 13b. Deposited 2018-05-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Not recorded | 22L 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one × 1 GO7 2-{[(3R,4S)-3-fluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}piperidin-4-yl]oxy}-4-(2-hydroxy-2-methylpropoxy)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；Compound 13b soaked for 30 min into preformed crystals of TrkA.
Well volume: 50.0 uL
Well Ingredients:
Polymer: 9.0 %w/v (9.0 uL of stock 50.0 %w/v) PEG 3350
Buffer: 15.8 %v/v (7.9 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Additive: 0.025 M (12.5 uL of stock 0.1 M) TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
Drop volume from well: 0.0050 uL
Drop protein volume: 0.34 uL
|
Resolution 2.53 Å R-free 0.225 |
| 6DKI Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19. Deposited 2018-05-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Not recorded | 22L 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one × 1 GOD 6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；Well volume: 20.0 uL
Well Ingredients:
Polymer: 9.0 %w/v (3.6 uL of stock 50.0 %w/v) PEG 3350
Buffer: 15.8 %v/v (3.16 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Additive: 0.025 M (5.0 uL of stock 0.1 M) TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
Drop volume from well: 0.01 uL
Drop protein volume: 0.2 uL
Protein: 6.30 mg/mL
|
Resolution 2.11 Å R-free 0.227 |
| 6IQN Crystal structure of TrkA kinase with ligand Deposited 2018-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
502–796（295 aa）
Chain B
502–796（295 aa）
|
Not recorded | AQ6 4-[[4-azanyl-3-(4-cyclohexylpiperazin-1-yl)-9,10-bis(oxidanylidene)anthracen-1-yl]amino]benzoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES pH6.5, 18% PEG 8000
|
Resolution 2.54 Å R-free 0.287 |
| 6J5L Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10e Deposited 2019-01-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
502–796（295 aa）
|
Not recorded | B9C N-{2-[({3-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indazol-5-yl}amino)methyl]phenyl}methanesulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.3；293 K；0.65 M Ammonium sulfate, 0.1 M Sodium Citrate pH 5.3
|
Resolution 2.30 Å R-free 0.251 |
| 6NPT TRK-A IN COMPLEX WITH LIGAND 1 Deposited 2019-01-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
393–697（305 aa）
Fragment：KINASE DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | KWY 4-tert-butyl-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；The protein at a concentration of 10 mg/ml was mixed with 2mM of the ligand (diluted from 100 mM DMSO stock solution) for 1 hour on ice and crystallized at 4 deg C (hanging drop) from:
0.10 M KH2PO4/ 0.10 M NaH2PO4/ 0.10 M MES/NaOH pH 6.00 and 1.90 M NaCl (cryo: 25% glycerol in reservoir), or
18.00 % (w/v) PEG 3350, 0.20 M CaCl2, 0.10 M, MES pH=6.50 (cryo: direct).
|
Resolution 2.19 Å R-free 0.276 |
| 6NSP TRK-A IN COMPLEX WITH LIGAND 9 Deposited 2019-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
402–698（297 aa）
Fragment：KINASE DOMAIN
|
Not recorded | L0P N-(8-methyl-2-phenylimidazo[1,2-a]pyridin-3-yl)-2-(3-oxo-2,3-dihydro-4H-1,4-benzothiazin-4-yl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M KH2PO4/ 0.1M NaH2PO4/ 0.1M MES/NaOH pH 6.0 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.1M, MES pH = 6.50 (cryo: direct).
|
Resolution 2.31 Å R-free 0.255 |
| 6NSS TRK-A IN COMPLEX WITH LIGAND 6 Deposited 2019-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
Fragment：KINASE DOMAIN
|
Not recorded | L0M N-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)-2-(10H-phenoxazin-10-yl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).
|
Resolution 1.97 Å R-free 0.218 |
| 6PL1 TRK-A IN COMPLEX WITH LIGAND 1B Deposited 2019-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
Fragment：KINASE DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OOJ N-(5-{[(7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-2-yl)methyl]sulfanyl}-1,3,4-thiadiazol-2-yl)-N'-[3-(trifluoromethyl)phenyl]urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl, pH=8.5, 50mM NaCl, 2mM DTT, 0.5mM PMSF
|
Resolution 2.03 Å R-free 0.260 |
| 6PL2 TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
Fragment：KINASE DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OOM N-(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)-2-{[1-(4-hydroxyphenyl)-1H-tetrazol-5-yl]sulfanyl}acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；20mM Tris/HCl
|
Resolution 2.59 Å R-free 0.274 |
| 6PL3 TRK-A IN COMPLEX WITH LIGAND 2a Deposited 2019-06-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
Fragment：KINASE DOMAIN
|
Not recorded | OOD 2-[(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)amino]-2-oxoethyl 4-(1H-tetrazol-1-yl)benzoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5
|
Resolution 3.00 Å R-free 0.272 |
| 6PL4 TRK-A IN COMPLEX WITH LIGAND 1 Deposited 2019-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
Fragment：KINASE DOMAIN
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OO7 N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；pH 8.5
|
Resolution 2.06 Å R-free 0.239 |
| 6PMA TRK-A IN COMPLEX WITH LIGAND Deposited 2019-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OQS N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[1-(4-methoxyphenyl)-4-oxo-1,4-dihydro-5H-pyrazolo[3,4-d]pyrimidin-5-yl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).
|
Resolution 2.53 Å R-free 0.266 |
| 6PMB TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-07-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
|
Not recorded | OQM 2-[5,7-dimethyl-2-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]-N-[3-(trifluoromethyl)phenyl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct)
|
Resolution 2.81 Å R-free 0.282 |
| 6PMC TRK-A IN COMPLEX WITH LIGAND 1a Deposited 2019-07-01 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
387–697（311 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | OQJ N-(6-{[(5-chloro-2-methoxyphenyl)carbamoyl]amino}-1,3-benzothiazol-2-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct)
|
Resolution 2.19 Å R-free 0.298 |
| 6PME TRK-A IN COMPLEX WITH LIGAND Deposited 2019-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric |
Chain A
387–697（311 aa）
Chain B
387–697（311 aa）
Chain C
387–697（311 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 12 OOY N-[2,4-bis(morpholin-4-yl)phenyl]-3-phenoxybenzamide × 12 SRT S,R MESO-TARTARIC ACID × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).
|
Resolution 3.00 Å R-free 0.315 |
| 7N3T TrkA ECD complex with designed miniprotein ligand Deposited 2021-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
36–382（347 aa）
Fragment：Extracellular domain, UNP residues 36-382
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；295 K；0.4 M ammonium sulfate, 0.1 M bis-tris pH 6.2, 16% PEG 3350.
|
Resolution 1.84 Å R-free 0.242 |
| 7N3T TrkA ECD complex with designed miniprotein ligand Deposited 2021-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
36–382（347 aa）
Fragment：Extracellular domain, UNP residues 36-382
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；295 K；0.4 M ammonium sulfate, 0.1 M bis-tris pH 6.2, 16% PEG 3350.
|
Resolution 1.84 Å R-free 0.242 |
| 7XAF The crystal structure of TrkA kinase in complex with 4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo- tetradecaphan-2-yne-45-carboxamide Deposited 2022-03-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
|
Not recorded | FKT 4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo-tetradecaphan-2-yne-45-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
|
Resolution 3.00 Å R-free 0.299 |
| 7XBI The crystal structure of human TrkA kinase bound to the inhibitor Deposited 2022-03-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
485–795（311 aa）
|
Not recorded | CVY 4-[[2-fluoranyl-5-(trifluoromethyl)phenyl]carbamoylamino]-~{N}-[3-(1-methylpyrazol-4-yl)-1~{H}-indazol-5-yl]-2-(trifluoromethyl)benzamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Na2HPO4/KH2PO4 pH=6.2, 2M NaCl
|
Resolution 2.16 Å R-free 0.246 |
| 8J5W The crystal structure of TrkA(F589L) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide Deposited 2023-04-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
484–796（313 aa）
|
Mutation：F589L | A4U N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
|
Resolution 2.28 Å R-free 0.266 |
| 8J5X The crystal structure of TrkA(G595R) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide Deposited 2023-04-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
|
Mutation：G595R | A4U N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
|
Resolution 2.09 Å R-free 0.220 |
| 8J61 The crystal structure of TrkA kinase in complex with 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide Deposited 2023-04-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
|
Not recorded | A0X 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
|
Resolution 3.05 Å R-free 0.255 |
| 8J63 The crystal structure of TrkA kinase in complex with 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-11-oxo-5-oxa-10,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide Deposited 2023-04-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
498–796（299 aa）
|
Not recorded | A6X 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-11-oxo-5-oxa-10,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
|
Resolution 3.00 Å R-free 0.289 |
| 8YTD Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides Deposited 2024-03-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
281–382（102 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；277 K；25% v/v ethylene glycol
|
Resolution 2.34 Å R-free 0.276 |
| 8YTE Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide Deposited 2024-03-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
281–382（102 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 GM1 AMINOMETHYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate
|
Resolution 2.26 Å R-free 0.249 |
| 8YTE Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide Deposited 2024-03-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
281–382（102 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 GM1 AMINOMETHYLAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate
|
Resolution 2.26 Å R-free 0.249 |
| 9DAI Crystal structure of Trk-A in complex with Staurosporin Deposited 2024-08-22 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
381–698（318 aa）
|
Mutation：T165E, S171E | STU STAUROSPORINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 30.0 uL
Well Ingredients:
Polymer: 10.0 %w/v PEG 3350
Buffer: 16.0 %v/v tacsimate (pH 8.00)
Organic (non-volatile): 10.0 %v/v Ethylene glycol
Additive: 0.025 M TCEP hydrochloride
Plate setup temperature: 13 C
Plate incubation temperature: 21 C
Drop volume from well: 0.2 uL
Drop protein volume: 0.4 uL (6.3mg/ml)
|
Resolution 2.86 Å R-free 0.277 |
59 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NTRK1_HUMAN |
| Isoform | P04629-4 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 3–320； UniProt 381–698 |
